.TH g_nmtraj 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_nmtraj - generate a virtual trajectory from an eigenvector

.B VERSION 4.5
.SH SYNOPSIS
\f3g_nmtraj\fP
.BI "\-s" " topol.tpr "
.BI "\-v" " eigenvec.trr "
.BI "\-o" " nmtraj.xtc "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-eignr" " string "
.BI "\-phases" " string "
.BI "\-temp" " real "
.BI "\-amplitude" " real "
.BI "\-nframes" " int "
.SH DESCRIPTION
\&\fB g_nmtraj\fR generates an virtual trajectory from an eigenvector, 
\&corresponding to a harmonic cartesian oscillation around the average 
\&structure. The eigenvectors should normally be mass\-weighted, but you can 
\&use non\-weighted eigenvectors to generate orthogonal motions. 
\&The output frames are written as a trajectory file covering an entire period, and 
\&the first frame is the average structure. If you write the trajectory in (or convert to) 
\&PDB format you can view it directly in PyMol and also render a photorealistic movie. 
\&Motion amplitudes are calculated from the eigenvalues and a preset temperature, 
\&assuming equipartition of the energy over all modes. To make the motion clearly visible 
\&in PyMol you might want to amplify it by setting an unrealistic high temperature. 
\&However, be aware that both the linear cartesian displacements and mass weighting will 
\&lead to serious structure deformation for high amplitudes \- this is is simply a limitation 
\&of the cartesian normal mode model. By default the selected eigenvector is set to 7, since 
\& the first six normal modes are the translational and rotational degrees of freedom.
.SH FILES
.BI "\-s" " topol.tpr" 
.B Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-v" " eigenvec.trr" 
.B Input
 Full precision trajectory: trr trj cpt 

.BI "\-o" " nmtraj.xtc" 
.B Output
 Trajectory: xtc trr trj gro g96 pdb 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-eignr"  " string" " 7" 
 String of eigenvectors to use (first is 1)

.BI "\-phases"  " string" " 0.0" 
 String of phases (default is 0.0)

.BI "\-temp"  " real" " 300   " 
 Temperature in Kelvin

.BI "\-amplitude"  " real" " 0.25  " 
 Amplitude for modes with eigenvalue=0

.BI "\-nframes"  " int" " 30" 
 Number of frames to generate

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
